NM_000053.4(ATP7B):c.1286-2A>G AND Wilson disease

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Dec 13, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001506996.4

Allele description [Variation Report for NM_000053.4(ATP7B):c.1286-2A>G]

NM_000053.4(ATP7B):c.1286-2A>G

Gene:

ATP7B:ATPase copper transporting beta [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q14.3

Genomic location:

Preferred name:

NM_000053.4(ATP7B):c.1286-2A>G

HGVS:

NC_000013.11:g.51970751T>C
NG_008806.1:g.45744A>G
NM_000053.4:c.1286-2A>GMANE SELECT
NM_001005918.3:c.1286-2A>G
NM_001243182.2:c.953-2A>G
NM_001330578.2:c.1286-2A>G
NM_001330579.2:c.1286-2A>G
NM_001406511.1:c.1286-2A>G
NM_001406512.1:c.1286-2A>G
NM_001406513.1:c.1286-2A>G
NM_001406514.1:c.1286-2A>G
NM_001406515.1:c.1286-2A>G
NM_001406516.1:c.1286-2A>G
NM_001406517.1:c.1190-2A>G
NM_001406518.1:c.1190-2A>G
NM_001406519.1:c.1286-2A>G
NM_001406520.1:c.1286-2A>G
NM_001406521.1:c.1286-2A>G
NM_001406522.1:c.1286-2A>G
NM_001406523.1:c.1286-2A>G
NM_001406524.1:c.1286-2A>G
NM_001406525.1:c.1286-2A>G
NM_001406526.1:c.1286-2A>G
NM_001406527.1:c.1286-2A>G
NM_001406528.1:c.1286-2A>G
NM_001406530.1:c.1190-2A>G
NM_001406531.1:c.1286-2A>G
NM_001406532.1:c.1286-2A>G
NM_001406534.1:c.1286-2A>G
NM_001406535.1:c.1286-2A>G
NM_001406536.1:c.1190-2A>G
NM_001406537.1:c.1286-2A>G
NM_001406538.1:c.1286-2A>G
NM_001406539.1:c.857-2A>G
NM_001406540.1:c.1286-2A>G
NM_001406541.1:c.1286-2A>G
NM_001406542.1:c.1286-2A>G
NM_001406543.1:c.1190-2A>G
NM_001406544.1:c.1190-2A>G
NM_001406545.1:c.1286-2A>G
NM_001406546.1:c.1286-2A>G
NM_001406547.1:c.1286-2A>G
NM_001406548.1:c.1285+3184A>G
NC_000013.10:g.52544887T>C
NM_000053.3:c.1286-2A>G

Links:

dbSNP: rs2139975409

NCBI 1000 Genomes Browser:

rs2139975409

Molecular consequence:

NM_001406548.1:c.1285+3184A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000053.4:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001005918.3:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001243182.2:c.953-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001330578.2:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001330579.2:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406511.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406512.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406513.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406514.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406515.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406516.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406517.1:c.1190-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406518.1:c.1190-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406519.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406520.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406521.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406522.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406523.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406524.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406525.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406526.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406527.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406528.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406530.1:c.1190-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406531.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406532.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406534.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406535.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406536.1:c.1190-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406537.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406538.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406539.1:c.857-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406540.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406541.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406542.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406543.1:c.1190-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406544.1:c.1190-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406545.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406546.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406547.1:c.1286-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Observations:

Condition(s)

Name:: Wilson disease (WND)
Synonyms:: Wilson's disease; Hepatolenticular degeneration
Identifiers:: MONDO: MONDO:0010200; MedGen: C0019202; Orphanet: 905; OMIM: 277900

Recent activity

Clear Turn Off Turn On

Rattus norvegicus methyltransferase like 26 (Mettl26), transcript variant 2, mRN...
Rattus norvegicus methyltransferase like 26 (Mettl26), transcript variant 2, mRNA
gi|2176733545|ref|NM_001037188.2|

Nucleotide
Homo sapiens collectin sub-family member 10 (C-type lectin), mRNA (cDNA clone MG...
Homo sapiens collectin sub-family member 10 (C-type lectin), mRNA (cDNA clone MGC:118794 IMAGE:40000432), complete cds
gi|74355533|gb|BC103815.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001711919	Inborn Errors of Metabolism Laboratory, Hospices Civils de Lyon	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 1, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 17949296, 25741868
SCV001977378	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Aug 10, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005053098	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 13, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001711919

Inborn Errors of Metabolism Laboratory, Hospices Civils de Lyon

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 1, 2021)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV001977378

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Aug 10, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005053098

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Dec 13, 2023)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Twenty-four novel mutations in Wilson disease patients of predominantly Italian origin.

Lepori MB, Lovicu M, Dessi V, Zappu A, Incollu S, Zancan L, Giacchino R, Iorio R, Vajro P, Maggiore G, Marcellini M, Barbera C, Pellecchia MT, Simonetti R, Kostic V, Farci AM, Solinas A, De Virgiliis S, Cao A, Loudianos G.

Genet Test. 2007 Fall;11(3):328-32.

PubMed [citation]

PMID:: 17949296

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Inborn Errors of Metabolism Laboratory, Hospices Civils de Lyon, SCV001711919.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From Genome-Nilou Lab, SCV001977378.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV005053098.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 17, 2024

ClinVar

Relating variation to medicine